When you attack a stack you get to choose the target, as long as the weapon type you are suing can attack it.
So in your example you are correct, an HE attack against that stack would only be able to target the BMP.
But is an M-1 was attacking, it could choose either the T-62 or the BMP.
Now, the best choice for the target, in this case would be the BMP because it's easier to kill and any "overflow" hits will automatically be tallied against the T-62.
So, it's not always, read: rarely, a good idea to stack weaker units with stronger ones....